PyClone-vi output

[DrBlanco-Heredia]

Dear Dr Dang,

The new version of PyClone (VI) gives the same CCF value in all variants sharing the same cluster per sample. Quoting the author of PyClone: "This is expected. The CCF quoted is the mean value of the cluster the mutation is assigned to. This differs from PyClone where we compute the mean value of the CCF across the MCMC samples. The latter better represents uncertainty over clustering, but I suspect it makes little difference in practice." This makes the box plots flat looking, since there's no variation inside clusters per sample (PDF attached). I believe this is not an issue for ClonEvol since the "infer.clonal.models" function takes precisely the mean value. I just want to be sure of it.

Thank you very much for your time and for this amazing tool.
Box_4Mets.pdf

[jsha129]

Dear developers, thanks for making this tool. I have a similar question to this one. pyclone-vi is much faster than pyclone. However, pyclone-vi only gives one CCF value for each clone. I assume pyclone would report CNA-corrected VAF for each mutation. Does the use of pyclone-vi change the results? Thanks